Experiment set3IT069 for Pseudomonas sp. RS175

Vanillic Acid carbon source 2.5 mM

Group: carbon source
Media: MME_noCarbon + Vanillic Acid (2.5 mM), pH=7
Culturing: Pseudomonas_RS175_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Joshua Elmore on 1-July-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 34 genes in this experiment

For carbon source Vanillic Acid in Pseudomonas sp. RS175

For carbon source Vanillic Acid across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Bacterial Chemotaxis	2
Terminal cytochrome C oxidases	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Flagellar motility	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Glycolate, glyoxylate interconversions	1
Histidine Degradation	1
Lipid A modifications	1
Lysine degradation	1
One-carbon metabolism by tetrahydropterines	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Purine conversions	1
Type IV pilus	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• One carbon pool by folate
• Fatty acid metabolism
• Oxidative phosphorylation
• Purine metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Histidine metabolism
• Tryptophan metabolism
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
arsenite to oxygen electron transfer	2	1	1
glycine degradation	3	3	1
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
formaldehyde oxidation VII (THF pathway)	4	4	1
L-histidine degradation I	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
L-histidine degradation II	5	5	1
L-histidine degradation III	6	4	1
Fe(II) oxidation	6	3	1
folate transformations I	13	9	2
L-histidine degradation VI	8	7	1
folate transformations III (E. coli)	9	9	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
photorespiration I	9	5	1
photorespiration III	9	5	1
photorespiration II	10	6	1
folate transformations II (plants)	11	10	1
purine nucleobases degradation I (anaerobic)	15	6	1
purine nucleobases degradation II (anaerobic)	24	16	1